Index

A

add_arg() (in module asap.pointmatch.generate_point_matches_spark) add_masks_to_lowres() (in module asap.rough_align.apply_rough_alignment_to_montages) add_match_collection_owner() (asap.em_montage_qc.schemas.DetectMontageDefectsParameters method) addMipMapsToRender() (in module asap.dataimport.apply_mipmaps_to_render) AddMipMapsToStack (class in asap.dataimport.apply_mipmaps_to_render) AddMipMapsToStackOutput (class in asap.dataimport.schemas) AddMipMapsToStackParameters (class in asap.dataimport.schemas) apply_rough_alignment() (in module asap.rough_align.apply_rough_alignment_to_montages) ApplyLensCorrection (class in asap.lens_correction.apply_lens_correction) ApplyLensCorrectionOutput (class in asap.lens_correction.schemas) ApplyLensCorrectionParameters (class in asap.lens_correction.schemas) ApplyRoughAlignmentException ApplyRoughAlignmentOutputParameters (class in asap.rough_align.schemas) ApplyRoughAlignmentTransform (class in asap.rough_align.apply_rough_alignment_to_montages) ApplyRoughAlignmentTransformParameters (class in asap.rough_align.schemas) asap module asap.dataimport module asap.dataimport.apply_mipmaps_to_render module asap.dataimport.create_mipmaps module asap.dataimport.generate_EM_tilespecs_from_metafile module asap.dataimport.generate_mipmaps module asap.dataimport.make_montage_scapes_stack module asap.dataimport.schemas module asap.em_montage_qc module asap.em_montage_qc.detect_montage_defects module asap.em_montage_qc.plots module asap.em_montage_qc.schemas module asap.intensity_correction module asap.intensity_correction.apply_multiplicative_correction module asap.intensity_correction.calculate_multiplicative_correction module asap.intensity_correction.schemas module asap.lens_correction module asap.lens_correction.apply_lens_correction module asap.lens_correction.schemas module asap.materialize module

asap.materialize.materialize_sections module asap.materialize.render_downsample_sections module asap.materialize.schemas module asap.module module asap.module.render_module module asap.module.schemas module asap.module.schemas.renderclient_schemas module asap.module.schemas.schemas module asap.module.schemas.spark_schemas module asap.module.schemas.stack_schemas module asap.module.template_module module asap.point_match_optimization module asap.point_match_optimization.schemas module asap.pointmatch module asap.pointmatch.create_tilepairs module asap.pointmatch.generate_point_matches_qsub module asap.pointmatch.generate_point_matches_spark module asap.pointmatch.schemas module asap.residuals module asap.residuals.compute_residuals module asap.rough_align module asap.rough_align.apply_rough_alignment_to_montages module asap.rough_align.schemas module asap.stack module asap.stack.consolidate_transforms module asap.stack.redirect_mipmaps module asap.stack.schemas module

B

Bounds (class in asap.materialize.schemas)

C

check_stack_for_mipmaps() (in module asap.materialize.render_downsample_sections) check_status_of_stack() (in module asap.em_montage_qc.detect_montage_defects) client_class (asap.pointmatch.create_tilepairs.TilePairClientModule attribute) client_script_name (asap.pointmatch.create_tilepairs.TilePairClientModule attribute) CollectionId (class in asap.pointmatch.schemas) compute_mean_tile_residuals() (in module asap.residuals.compute_residuals) compute_residuals_within_group() (in module asap.residuals.compute_residuals) consolidate_transforms() (in module asap.stack.consolidate_transforms) ConsolidateTransforms (class in asap.stack.consolidate_transforms)

ConsolidateTransformsOutputParameters (class in asap.stack.schemas) ConsolidateTransformsParameters (class in asap.stack.schemas) create_mipmap_from_tuple() (in module asap.dataimport.generate_mipmaps) create_mipmap_from_tuple_uri() (in module asap.dataimport.generate_mipmaps) create_mipmaps() (in module asap.dataimport.create_mipmaps) create_mipmaps_legacy() (in module asap.dataimport.create_mipmaps) create_mipmaps_uri() (in module asap.dataimport.create_mipmaps) create_montage_scape_tile_specs() (in module asap.dataimport.make_montage_scapes_stack) create_tilespecs_without_mipmaps() (in module asap.materialize.render_downsample_sections) CreateMipMapException

D

default_output_schema (asap.dataimport.apply_mipmaps_to_render.AddMipMapsToStack attribute) (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule attribute) (asap.dataimport.generate_mipmaps.GenerateMipMaps attribute) (asap.dataimport.make_montage_scapes_stack.MakeMontageScapeSectionStack attribute) (asap.em_montage_qc.detect_montage_defects.DetectMontageDefectsModule attribute) (asap.lens_correction.apply_lens_correction.ApplyLensCorrection attribute) (asap.materialize.materialize_sections.MaterializeSectionsModule attribute) (asap.materialize.render_downsample_sections.RenderSectionAtScale attribute) (asap.module.template_module.TemplateModule attribute) (asap.pointmatch.create_tilepairs.TilePairClientModule attribute) (asap.pointmatch.generate_point_matches_spark.PointMatchClientModuleSpark attribute) (asap.rough_align.apply_rough_alignment_to_montages.ApplyRoughAlignmentTransform attribute) (asap.stack.consolidate_transforms.ConsolidateTransforms attribute) (asap.stack.redirect_mipmaps.RedirectMipMapsModule attribute) default_schema (asap.dataimport.apply_mipmaps_to_render.AddMipMapsToStack attribute) (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule attribute) (asap.dataimport.generate_mipmaps.GenerateMipMaps attribute) (asap.dataimport.make_montage_scapes_stack.MakeMontageScapeSectionStack attribute) (asap.em_montage_qc.detect_montage_defects.DetectMontageDefectsModule attribute) (asap.intensity_correction.apply_multiplicative_correction.MultIntensityCorr attribute) (asap.intensity_correction.calculate_multiplicative_correction.MakeMedian attribute) (asap.lens_correction.apply_lens_correction.ApplyLensCorrection attribute) (asap.materialize.materialize_sections.MaterializeSectionsModule attribute) (asap.materialize.render_downsample_sections.RenderSectionAtScale attribute) (asap.module.render_module.RenderModule attribute) (asap.module.render_module.SparkModule attribute) (asap.module.render_module.StackInputModule attribute) (asap.module.render_module.StackOutputModule attribute) (asap.module.template_module.TemplateModule attribute) (asap.pointmatch.create_tilepairs.TilePairClientModule attribute) (asap.pointmatch.generate_point_matches_spark.PointMatchClientModuleSpark attribute) (asap.rough_align.apply_rough_alignment_to_montages.ApplyRoughAlignmentTransform attribute) (asap.stack.consolidate_transforms.ConsolidateTransforms attribute) (asap.stack.redirect_mipmaps.RedirectMipMapsModule attribute)

delete_zValues() (asap.module.render_module.StackOutputModule method) DeleteMaterializedSectionsOutput (class in asap.materialize.schemas) DeleteMaterializedSectionsParameters (class in asap.materialize.schemas) dereference_tforms() (in module asap.stack.consolidate_transforms) detect_disconnected_tiles() (in module asap.em_montage_qc.detect_montage_defects) detect_distortion() (in module asap.em_montage_qc.detect_montage_defects) detect_seams() (in module asap.em_montage_qc.detect_montage_defects) detect_stitching_gaps() (in module asap.em_montage_qc.detect_montage_defects) detect_stitching_mistakes() (in module asap.em_montage_qc.detect_montage_defects) DetectDistortionParameters (class in asap.em_montage_qc.schemas) DetectDistortionParametersOutput (class in asap.em_montage_qc.schemas) DetectMontageDefectsModule (class in asap.em_montage_qc.detect_montage_defects) DetectMontageDefectsParameters (class in asap.em_montage_qc.schemas) DetectMontageDefectsParametersOutput (class in asap.em_montage_qc.schemas) directory_to_prefix() (asap.dataimport.schemas.GenerateMipMapsParameters method) downsample_specific_mipmapLevel() (asap.materialize.render_downsample_sections.RenderSectionAtScale class method) DownsampleMaskHandlerSchema (class in asap.rough_align.schemas)

F

FeatureExtractionParameters (class in asap.module.schemas.renderclient_schemas) FeatureRenderClipParameters (class in asap.module.schemas.renderclient_schemas) FeatureRenderParameters (class in asap.module.schemas.renderclient_schemas) FeatureStorageParameters (class in asap.module.schemas.renderclient_schemas)

filter_highres_with_masks() (in module asap.rough_align.apply_rough_alignment_to_montages) fix_badkey() (asap.module.schemas.stack_schemas.OverridableParameterSchema static method) flatten_and_dereference_tforms() (in module asap.stack.consolidate_transforms) flatten_tforms() (in module asap.stack.consolidate_transforms) form_sift_params_list() (in module asap.pointmatch.generate_point_matches_spark)

G

generate_zValues() (asap.module.schemas.stack_schemas.ZValueParameters method) GenerateEMTileSpecsModule (class in asap.dataimport.generate_EM_tilespecs_from_metafile) GenerateEMTileSpecsOutput (class in asap.dataimport.schemas) GenerateEMTileSpecsParameters (class in asap.dataimport.schemas) GenerateMipMaps (class in asap.dataimport.generate_mipmaps) GenerateMipMapsOutput (class in asap.dataimport.schemas) GenerateMipMapsParameters (class in asap.dataimport.schemas) get_args() (asap.materialize.materialize_sections.MaterializeSectionsModule class method) (asap.module.render_module.SparkModule class method) (asap.pointmatch.generate_point_matches_spark.PointMatchClientModuleSpark class method) get_cmd_opt() (asap.module.render_module.SparkModule static method) get_filepath_from_tilespec() (in module asap.dataimport.generate_mipmaps) get_flag_cmd() (asap.module.render_module.SparkModule static method)

get_host_port_dict_from_url() (in module asap.pointmatch.generate_point_matches_spark) get_inputstack_zs() (asap.module.render_module.StackInputModule method) get_mask_paths() (in module asap.rough_align.apply_rough_alignment_to_montages) get_materialize_options() (asap.materialize.materialize_sections.MaterializeSectionsModule class method) get_overlapping_inputstack_zvalues() (asap.module.render_module.StackInputModule method) get_pointmatch_args() (asap.pointmatch.generate_point_matches_spark.PointMatchClientModuleSpark class method) get_pre_post_tspecs() (in module asap.em_montage_qc.detect_montage_defects) get_replacement_ImagePyramid() (asap.stack.redirect_mipmaps.RedirectMipMapsModule static method) get_spark_call() (asap.module.render_module.SparkModule class method) get_spark_command() (asap.module.render_module.SparkModule class method) get_tile_centers() (in module asap.residuals.compute_residuals) getImage() (in module asap.intensity_correction.apply_multiplicative_correction) getImageFromTilespecs() (in module asap.intensity_correction.calculate_multiplicative_correction)

I

image_coords_from_stage() (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule static method) image_directory_to_prefix() (asap.dataimport.schemas.GenerateEMTileSpecsParameters method)

input_stacks (asap.em_montage_qc.schemas.DetectDistortionParameters attribute) InputStackParameters (class in asap.module.schemas.stack_schemas) intensity_corr() (in module asap.intensity_correction.apply_multiplicative_correction)

L

LowresStackParameters (class in asap.rough_align.schemas)

M

make_median_image() (in module asap.intensity_correction.calculate_multiplicative_correction) make_tilespecs_and_cmds() (in module asap.dataimport.generate_mipmaps) MakeAnchorStackSchema (class in asap.rough_align.schemas) MakeMedian (class in asap.intensity_correction.calculate_multiplicative_correction) MakeMedianParams (class in asap.intensity_correction.schemas) MakeMontageScapeSectionStack (class in asap.dataimport.make_montage_scapes_stack) MakeMontageScapeSectionStackOutput (class in asap.dataimport.schemas) MakeMontageScapeSectionStackParameters (class in asap.dataimport.schemas) maskUrl_to_uri() (asap.dataimport.schemas.GenerateEMTileSpecsParameters method) (asap.lens_correction.schemas.ApplyLensCorrectionParameters method) MatchDerivationParameters (class in asap.module.schemas.renderclient_schemas) MatchWebServiceParameters (class in asap.module.schemas.renderclient_schemas) MaterializedBoxParameters (class in asap.module.schemas.renderclient_schemas) MaterializeSectionsError MaterializeSectionsModule (class in asap.materialize.materialize_sections) MaterializeSectionsOutput (class in asap.materialize.schemas) MaterializeSectionsParameters (class in asap.materialize.schemas) metafile_to_uri() (asap.dataimport.schemas.GenerateEMTileSpecsParameters method) mipmap_block_reduce() (in module asap.dataimport.create_mipmaps) mipmap_directory_to_prefix() (asap.dataimport.schemas.AddMipMapsToStackParameters method) mipmap_PIL() (in module asap.dataimport.create_mipmaps) MipMapDirectories (class in asap.stack.schemas) module asap asap.dataimport asap.dataimport.apply_mipmaps_to_render asap.dataimport.create_mipmaps asap.dataimport.generate_EM_tilespecs_from_metafile asap.dataimport.generate_mipmaps asap.dataimport.make_montage_scapes_stack asap.dataimport.schemas asap.em_montage_qc asap.em_montage_qc.detect_montage_defects asap.em_montage_qc.plots asap.em_montage_qc.schemas asap.intensity_correction asap.intensity_correction.apply_multiplicative_correction asap.intensity_correction.calculate_multiplicative_correction asap.intensity_correction.schemas asap.lens_correction asap.lens_correction.apply_lens_correction asap.lens_correction.schemas asap.materialize asap.materialize.materialize_sections asap.materialize.render_downsample_sections asap.materialize.schemas asap.module asap.module.render_module asap.module.schemas asap.module.schemas.renderclient_schemas asap.module.schemas.schemas asap.module.schemas.spark_schemas asap.module.schemas.stack_schemas asap.module.template_module asap.point_match_optimization asap.point_match_optimization.schemas asap.pointmatch asap.pointmatch.create_tilepairs asap.pointmatch.generate_point_matches_qsub asap.pointmatch.generate_point_matches_spark asap.pointmatch.schemas asap.residuals asap.residuals.compute_residuals asap.rough_align asap.rough_align.apply_rough_alignment_to_montages asap.rough_align.schemas asap.stack asap.stack.consolidate_transforms asap.stack.redirect_mipmaps asap.stack.schemas

MultIntensityCorr (class in asap.intensity_correction.apply_multiplicative_correction) MultIntensityCorrParams (class in asap.intensity_correction.schemas)

O

opts (asap.dataimport.schemas.AddMipMapsToStackOutput attribute) (asap.dataimport.schemas.AddMipMapsToStackParameters attribute) (asap.dataimport.schemas.GenerateEMTileSpecsOutput attribute) (asap.dataimport.schemas.GenerateEMTileSpecsParameters attribute) (asap.dataimport.schemas.GenerateMipMapsOutput attribute) (asap.dataimport.schemas.GenerateMipMapsParameters attribute) (asap.dataimport.schemas.MakeMontageScapeSectionStackOutput attribute) (asap.dataimport.schemas.MakeMontageScapeSectionStackParameters attribute) (asap.em_montage_qc.schemas.DetectDistortionParameters attribute) (asap.em_montage_qc.schemas.DetectDistortionParametersOutput attribute) (asap.em_montage_qc.schemas.DetectMontageDefectsParameters attribute) (asap.em_montage_qc.schemas.DetectMontageDefectsParametersOutput attribute) (asap.em_montage_qc.schemas.RoughQCOutputSchema attribute) (asap.em_montage_qc.schemas.RoughQCSchema attribute) (asap.intensity_correction.schemas.MakeMedianParams attribute) (asap.intensity_correction.schemas.MultIntensityCorrParams attribute) (asap.lens_correction.schemas.ApplyLensCorrectionOutput attribute) (asap.lens_correction.schemas.ApplyLensCorrectionParameters attribute) (asap.lens_correction.schemas.TransformParameters attribute) (asap.materialize.schemas.Bounds attribute) (asap.materialize.schemas.DeleteMaterializedSectionsOutput attribute) (asap.materialize.schemas.DeleteMaterializedSectionsParameters attribute) (asap.materialize.schemas.MaterializeSectionsOutput attribute) (asap.materialize.schemas.MaterializeSectionsParameters attribute) (asap.materialize.schemas.RenderSectionAtScaleOutput attribute) (asap.materialize.schemas.RenderSectionAtScaleParameters attribute) (asap.materialize.schemas.ValidateMaterializationOutput attribute) (asap.materialize.schemas.ValidateMaterializationParameters attribute) (asap.module.schemas.renderclient_schemas.FeatureExtractionParameters attribute) (asap.module.schemas.renderclient_schemas.FeatureRenderClipParameters attribute) (asap.module.schemas.renderclient_schemas.FeatureRenderParameters attribute) (asap.module.schemas.renderclient_schemas.FeatureStorageParameters attribute) (asap.module.schemas.renderclient_schemas.MatchDerivationParameters attribute) (asap.module.schemas.renderclient_schemas.MatchWebServiceParameters attribute) (asap.module.schemas.renderclient_schemas.MaterializedBoxParameters attribute) (asap.module.schemas.renderclient_schemas.RenderParametersMatchWebServiceParameters attribute) (asap.module.schemas.renderclient_schemas.RenderParametersRenderWebServiceParameters attribute) (asap.module.schemas.renderclient_schemas.RenderWebServiceParameters attribute) (asap.module.schemas.renderclient_schemas.WebServiceParameters attribute) (asap.module.schemas.renderclient_schemas.ZRangeParameters attribute) (asap.module.schemas.schemas.RenderClientParameters attribute) (asap.module.schemas.schemas.RenderParameters attribute) (asap.module.schemas.schemas.TemplateOutputParameters attribute) (asap.module.schemas.schemas.TemplateParameters attribute) (asap.module.schemas.spark_schemas.SparkOptions attribute) (asap.module.schemas.spark_schemas.SparkParameters attribute) (asap.module.schemas.stack_schemas.InputStackParameters attribute) (asap.module.schemas.stack_schemas.OutputStackParameters attribute) (asap.module.schemas.stack_schemas.OverridableParameterSchema attribute) (asap.module.schemas.stack_schemas.ProcessPoolParameters attribute) (asap.module.schemas.stack_schemas.RenderCycle attribute) (asap.module.schemas.stack_schemas.RenderMipMapPathBuilder attribute) (asap.module.schemas.stack_schemas.RenderStackVersion attribute) (asap.module.schemas.stack_schemas.StackTransitionParameters attribute) (asap.module.schemas.stack_schemas.ZValueParameters attribute) (asap.point_match_optimization.schemas.PointMatchOptimizationParameters attribute) (asap.point_match_optimization.schemas.PointMatchOptimizationParametersOutput attribute) (asap.point_match_optimization.schemas.PtMatchOptimizationParameters attribute) (asap.point_match_optimization.schemas.PtMatchOptimizationParametersOutput attribute) (asap.point_match_optimization.schemas.SIFT_options attribute) (asap.point_match_optimization.schemas.url_options attribute) (asap.pointmatch.schemas.CollectionId attribute) (asap.pointmatch.schemas.PointMatchClientOutputSchema attribute) (asap.pointmatch.schemas.PointMatchClientParametersQsub attribute) (asap.pointmatch.schemas.PointMatchClientParametersSpark attribute) (asap.pointmatch.schemas.PointMatchOpenCVParameters attribute) (asap.pointmatch.schemas.SIFTPointMatchParameters attribute) (asap.pointmatch.schemas.SwapPointMatches attribute) (asap.pointmatch.schemas.SwapPointMatchesOutput attribute) (asap.pointmatch.schemas.TilePairClientOutputParameters attribute) (asap.pointmatch.schemas.TilePairClientParameters attribute) (asap.rough_align.schemas.ApplyRoughAlignmentOutputParameters attribute) (asap.rough_align.schemas.ApplyRoughAlignmentTransformParameters attribute) (asap.rough_align.schemas.DownsampleMaskHandlerSchema attribute) (asap.rough_align.schemas.LowresStackParameters attribute) (asap.rough_align.schemas.MakeAnchorStackSchema attribute) (asap.rough_align.schemas.OutputLowresStackParameters attribute) (asap.rough_align.schemas.PairwiseRigidOutputSchema attribute) (asap.rough_align.schemas.PairwiseRigidSchema attribute) (asap.rough_align.schemas.PointMatchCollectionParameters attribute) (asap.stack.schemas.ConsolidateTransformsOutputParameters attribute) (asap.stack.schemas.ConsolidateTransformsParameters attribute) (asap.stack.schemas.MipMapDirectories attribute) (asap.stack.schemas.RedirectMipMapsOutput attribute) (asap.stack.schemas.RedirectMipMapsParameters attribute) (asap.stack.schemas.RemapZsOutput attribute) (asap.stack.schemas.RemapZsParameters attribute) (asap.stack.schemas.SwapZsOutput attribute) (asap.stack.schemas.SwapZsParameters attribute)

output_tilespecs_to_stack() (asap.module.render_module.StackOutputModule method) OutputLowresStackParameters (class in asap.rough_align.schemas) OutputStackParameters (class in asap.module.schemas.stack_schemas) OverridableParameterSchema (class in asap.module.schemas.stack_schemas) override_input() (asap.module.schemas.stack_schemas.OverridableParameterSchema method)

P

PairwiseRigidOutputSchema (class in asap.rough_align.schemas) PairwiseRigidSchema (class in asap.rough_align.schemas) plot_defects() (in module asap.em_montage_qc.plots) plot_residual() (in module asap.em_montage_qc.plots) plot_section_maps() (in module asap.em_montage_qc.plots) point_match_plot() (in module asap.em_montage_qc.plots) PointMatchClientModuleQsub (class in asap.pointmatch.generate_point_matches_qsub) PointMatchClientModuleSpark (class in asap.pointmatch.generate_point_matches_spark) PointMatchClientOutputSchema (class in asap.pointmatch.schemas) PointMatchClientParametersQsub (class in asap.pointmatch.schemas)

PointMatchClientParametersSpark (class in asap.pointmatch.schemas) PointMatchCollectionParameters (class in asap.rough_align.schemas) PointMatchOpenCVParameters (class in asap.pointmatch.schemas) PointMatchOptimizationParameters (class in asap.point_match_optimization.schemas) PointMatchOptimizationParametersOutput (class in asap.point_match_optimization.schemas) process_tile() (in module asap.intensity_correction.apply_multiplicative_correction) process_z() (in module asap.stack.consolidate_transforms) ProcessPoolParameters (class in asap.module.schemas.stack_schemas) PtMatchOptimizationParameters (class in asap.point_match_optimization.schemas) PtMatchOptimizationParametersOutput (class in asap.point_match_optimization.schemas)

R

randomly_subsample_tilespecs() (in module asap.intensity_correction.calculate_multiplicative_correction) RedirectMipMapsModule (class in asap.stack.redirect_mipmaps) RedirectMipMapsOutput (class in asap.stack.schemas) RedirectMipMapsParameters (class in asap.stack.schemas) RemapZsOutput (class in asap.stack.schemas) RemapZsParameters (class in asap.stack.schemas) RenderClientParameters (class in asap.module.schemas.schemas) RenderCycle (class in asap.module.schemas.stack_schemas) RenderMipMapPathBuilder (class in asap.module.schemas.stack_schemas) RenderModule (class in asap.module.render_module) RenderModuleException RenderParameters (class in asap.module.schemas.schemas) RenderParametersMatchWebServiceParameters (class in asap.module.schemas.renderclient_schemas) RenderParametersRenderWebServiceParameters (class in asap.module.schemas.renderclient_schemas) RenderSectionAtScale (class in asap.materialize.render_downsample_sections) RenderSectionAtScaleOutput (class in asap.materialize.schemas) RenderSectionAtScaleParameters (class in asap.materialize.schemas) RenderStackVersion (class in asap.module.schemas.stack_schemas) RenderWebServiceParameters (class in asap.module.schemas.renderclient_schemas) RoughQCOutputSchema (class in asap.em_montage_qc.schemas)

RoughQCSchema (class in asap.em_montage_qc.schemas) run() (asap.dataimport.apply_mipmaps_to_render.AddMipMapsToStack method) (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule method) (asap.dataimport.generate_mipmaps.GenerateMipMaps method) (asap.dataimport.make_montage_scapes_stack.MakeMontageScapeSectionStack method) (asap.em_montage_qc.detect_montage_defects.DetectMontageDefectsModule method) (asap.intensity_correction.apply_multiplicative_correction.MultIntensityCorr method) (asap.intensity_correction.calculate_multiplicative_correction.MakeMedian method) (asap.lens_correction.apply_lens_correction.ApplyLensCorrection method) (asap.materialize.materialize_sections.MaterializeSectionsModule method) (asap.materialize.render_downsample_sections.RenderSectionAtScale method) (asap.module.template_module.TemplateModule method) (asap.pointmatch.create_tilepairs.TilePairClientModule method) (asap.pointmatch.generate_point_matches_qsub.PointMatchClientModuleQsub method) (asap.pointmatch.generate_point_matches_spark.PointMatchClientModuleSpark method) (asap.rough_align.apply_rough_alignment_to_montages.ApplyRoughAlignmentTransform method) (asap.stack.consolidate_transforms.ConsolidateTransforms method) (asap.stack.redirect_mipmaps.RedirectMipMapsModule method) run_analysis() (in module asap.em_montage_qc.detect_montage_defects) run_spark_command() (asap.module.render_module.SparkModule method)

S

sanitize_cmd() (asap.module.render_module.SparkModule static method) sectionId_from_z() (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule static method) SIFT_options (class in asap.point_match_optimization.schemas) SIFTPointMatchParameters (class in asap.pointmatch.schemas) SparkModule (class in asap.module.render_module) SparkModuleError SparkOptions (class in asap.module.schemas.spark_schemas) SparkParameters (class in asap.module.schemas.spark_schemas)

StackInputModule (class in asap.module.render_module) StackOutputModule (class in asap.module.render_module) StackTransitionModule (class in asap.module.render_module) StackTransitionParameters (class in asap.module.schemas.stack_schemas) SwapPointMatches (class in asap.pointmatch.schemas) SwapPointMatchesOutput (class in asap.pointmatch.schemas) SwapZsOutput (class in asap.stack.schemas) SwapZsParameters (class in asap.stack.schemas)

T

TemplateModule (class in asap.module.template_module) TemplateOutputParameters (class in asap.module.schemas.schemas) TemplateParameters (class in asap.module.schemas.schemas) threshold_cutoff (asap.em_montage_qc.schemas.DetectDistortionParameters attribute) tileId_from_basename() (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule method)

TilePairClientModule (class in asap.pointmatch.create_tilepairs) TilePairClientOutputParameters (class in asap.pointmatch.schemas) TilePairClientParameters (class in asap.pointmatch.schemas) TransformParameters (class in asap.lens_correction.schemas) ts_from_imgdata() (asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule method)

U

url_options (class in asap.point_match_optimization.schemas)

V

validate_data() (asap.dataimport.schemas.MakeMontageScapeSectionStackParameters method) (asap.materialize.schemas.RenderSectionAtScaleParameters method) (asap.point_match_optimization.schemas.PtMatchOptimizationParameters method) (asap.pointmatch.schemas.TilePairClientParameters method) (asap.rough_align.schemas.ApplyRoughAlignmentTransformParameters method)

validate_options() (asap.module.schemas.renderclient_schemas.RenderParametersMatchWebServiceParameters method) (asap.module.schemas.renderclient_schemas.RenderParametersRenderWebServiceParameters method) validate_tilespecs() (asap.module.render_module.StackOutputModule method) ValidateMaterializationOutput (class in asap.materialize.schemas) ValidateMaterializationParameters (class in asap.materialize.schemas) validationOptions() (asap.dataimport.schemas.GenerateMipMapsParameters class method)

W

WebServiceParameters (class in asap.module.schemas.renderclient_schemas) WithThreadPool (class in asap.materialize.render_downsample_sections)

write_image() (in module asap.intensity_correction.apply_multiplicative_correction) writeImage() (in module asap.dataimport.create_mipmaps)

Z

ZRangeParameters (class in asap.module.schemas.renderclient_schemas)

ZValueParameters (class in asap.module.schemas.stack_schemas)